BioGRID

BioGRID#

BioGRID[1] is one of the most widely-used databases that catalogues protein-protein interactions. In version 4.4.223, the database is constructed by going through more than 80,000 publications, which has 2,629,002 protein and genetic interactions.

According to the BioGRID database, transmembrane proteins are involved in nearly a quarter of all confirmed human interactions, and an even higher percentage (almost 40%) was identified based on the most recent human interactome map[2].

TMKit offers an interface, tmkit.ppi, to access the database. In this tutorial, we will show how we can use this database in Python, starting from downloading it.

Example usage#

First, let’s download the BioGRID database. In the example dataset, there is a folder called ppi. The path is ./data/ppi/, which is the place where we suggest users to manage the data used and generated. We can choose a specific version of the database, namely, 4.4.212 and save it in ./data/ppi/ through parameter sv_fp.

You should have a file called BIOGRID-ALL-4.4.212.tab3.zip after downloading. The tmk.ppi.download_biogrid_db function will automatically decompress it as BIOGRID-ALL-4.4.212.tab3.txt.

import tmkit as tmk

tmk.ppi.download_biogrid_db(
    version='4.4.212',
    sv_fp='./data/ppi/',
)

Then, using the following codes, you can access the database. The data/ppi/BIOGRID-ALL-4.4.212.tab3.txt is the BioGRID database. The tmk.ppi.read_biogrid_db function will extract a subset of it containing only protein interactors A and B (SWISS-PROT Accessions Interactor A and SWISS-PROT Accessions Interactor B).

Importantly, this function will save the subset as in BIOGRID-ALL-4.4.212.biogrid in ./data/ppi/BIOGRID-ALL-4.4.212.biogrid.

import tmkit as tmk

df = tmk.ppi.read_biogrid_db(
    biogrid_fpn='data/ppi/BIOGRID-ALL-4.4.212.tab3.txt',
    sv_fpn='data/ppi/BIOGRID-ALL-4.4.212.biogrid',
    extract_ids=[
        'SWISS-PROT Accessions Interactor A',
        'SWISS-PROT Accessions Interactor B',
    ],
)
print(df)

Attributes#

Attribute

Description

version

version of a BioGRID database, for example, 4.4.212.

biogrid_fpn

path where a BioGRID database is placed

sv_fp

path to where you want to save files

extract_ids

a list that can include more than one feature, such as SWISS-PROT Accessions Interactor A and SWISS-PROT Accessions Interactor B

See also

Please see here for better understanding the file-naming system.

Output#

Finally, you will see the following output, which shows 37 features in BioGRID, for example Entrez Gene Interactor A. You can extract each of the feature in Python, e.g., df['SWISS-PROT Accessions Interactor A'].

======>reading BioGRID...
======>BioGRID features are:
=========>No.1: #BioGRID Interaction ID
=========>No.2: Entrez Gene Interactor A
=========>No.3: Entrez Gene Interactor B
=========>No.4: BioGRID ID Interactor A
=========>No.5: BioGRID ID Interactor B
=========>No.6: Systematic Name Interactor A
=========>No.7: Systematic Name Interactor B
=========>No.8: Official Symbol Interactor A
=========>No.9: Official Symbol Interactor B
=========>No.10: Synonyms Interactor A
=========>No.11: Synonyms Interactor B
=========>No.12: Experimental System
=========>No.13: Experimental System Type
=========>No.14: Author
=========>No.15: Publication Source
=========>No.16: Organism ID Interactor A
=========>No.17: Organism ID Interactor B
=========>No.18: Throughput
=========>No.19: Score
=========>No.20: Modification
=========>No.21: Qualifications
=========>No.22: Tags
=========>No.23: Source Database
=========>No.24: SWISS-PROT Accessions Interactor A
=========>No.25: TREMBL Accessions Interactor A
=========>No.26: REFSEQ Accessions Interactor A
=========>No.27: SWISS-PROT Accessions Interactor B
=========>No.28: TREMBL Accessions Interactor B
=========>No.29: REFSEQ Accessions Interactor B
=========>No.30: Ontology Term IDs
=========>No.31: Ontology Term Names
=========>No.32: Ontology Term Categories
=========>No.33: Ontology Term Qualifier IDs
=========>No.34: Ontology Term Qualifier Names
=========>No.35: Ontology Term Types
=========>No.36: Organism Name Interactor A
=========>No.37: Organism Name Interactor B
======>The file is saved.
        SWISS-PROT Accessions Interactor A SWISS-PROT Accessions Interactor B
0                                   P45985                             Q14315
1                                   Q86TC9                             P35609
2                                   Q04771                             P49354
3                                   P23769                             P29590
4                                   P15927                             P40763
...                                    ...                                ...
2407708                             P0DTC2                             P53622
2407709                             P0DTC2                             Q96WV5
2407710                             P38260                             P11484
2407711                             P38260                             P32589
2407712                             P59594                             P53621

[2407713 rows x 2 columns]
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